Srm methods in alzheimer&#39;s disease and neurological disease assays

ABSTRACT

Provided herein are methods for developing selected reaction monitoring mass spectrometry (LC-SRM-MS) assays.

RELATED APPLICATIONS

This application claims priority and benefit of U.S. ProvisionalApplication No. 61/620,770, filed Apr. 5, 2012, the contents of which isincorporated by reference in it's entirety.

BACKGROUND

Liquid Chromatography Selected Reaction Monitoring Mass Spectrometry(LC-SRM-MS) has emerged as an alternative technology to immunoassays forquantification of target proteins in biological samples. LC-SRM-MSmethods are highly desirable because LC-SRM-MS methods provide bothabsolute structural specificity for the target protein and relative orabsolute measurement of the target protein concentration when suitableinternal standards are utilized. In contrast to immunoassays, LC-SRM-MSdoes not involve the manufacturing of biologics. LC-SRM-MS proteinassays can be rapidly and inexpensively developed in contrast to thedevelopment of immunoassays. LC-SRM-MS are highly multiplexed, withsimultaneous assays for hundreds of proteins performed in a singlesample analysis. Using LC-SRM-MS in contrast to other proteomictechnologies allows for complex assays for the identification diagnosticproteins in complex diseases such as cancer, autoimmune, and metabolicdisease. In particular, the development of a highly multiplexedLC-SRM-MS assay that reproducibly identifies a specific set of proteinsrelevant to a clinical disease presents diagnostic advantages andefficiencies. To date, proteomic techniques have not enabled such assaysto exist where hundreds of proteins can be accurately quantified withina single sample. The present disclosure provides accurate measurement ofhundreds of Alzheimer's disease associated proteins within a singlesample using multiplexed techniques.

SUMMARY

The present disclosure provides a LC-SRM-MS assay for the measurement ofat least 357 Alzheimer's disease associated proteins in a single sampleand in a single LC-SRM-MS assay. The assay was optimized for proteinquantification and minimal interference among proteins in the assay.This LC-SRM-MS assay is novel because measurement of a large number ofproteins in a single sample specifically associated with Alzheimer'sdisease has not been accomplished. Simultaneous measurement of such alarge number of proteins without interference among the proteinsrequires specific techniques to distinguish among the proteins. Thecurrent disclosure provides clinical utility as this assay was used fordevelopment of Alzheimer's disease diagnostic tests for the earlydetection of Alzheimer's disease, managing disease treatment, as well astesting for disease recurrence.

The object of the present disclosure is to provide improved methods forthe use of LC-SRM-MS in the development of assays. Accordingly, providedherein is a method for developing peptides and transitions for aplurality of at least 200 proteins for a single sample selected reactionmonitoring mass spectrometry (LC-SRM-MS) assay, including the steps ofproviding a set of 200 or more proteins; generating transitions for eachprotein; determining the Mascot score for SRM-triggered tandem massspectrometry (MS/MS) spectra; performing collision energy optimizationon the transitions; selecting peptides with transitions showing thegreatest peak areas of their transitions; selecting a set of transitionsfor each peptide, wherein the transitions for each peptide have one ofthe four most intense b or y transition ions; the transitions for eachpeptide have m/z values of at least 30 m/z above or below those of theprecursor ion; the transitions for each peptide do not interfere withtransitions from other peptides; and the transitions representtransitions due to breakage of peptide bond at different sites of theprotein.

In one embodiment of the method, each selected peptide in the set ofpeptides has a monoisotopic mass of 700-5000 Da; and does not contain acysteine or a methionine or does not contain cysteine or methionine. Inother embodiments, each selected peptide contains cysteine ormethionine. In another embodiment, the transitions for each peptide haveone of the four most intense b or y transition ions; have m/z values ofat least 30 m/z above or below those of a precursor ion; do notinterfere with transitions from other peptides; and representtransitions due to breakage of peptide bond at different sites of theprotein.

In another embodiment of the method, the peptides do not include anypeptide that is bounded by KK, KR, RK or RR (either upstream ordownstream) in the corresponding protein sequence. Specifically, theamino acid is charged at pH 7.0. In another embodiment, each peptide ofsaid set of peptides is unique to the corresponding protein. In yetanother embodiment, the peptides do not include peptides which wereobserved in post-translational modified forms. In still anotherembodiment, each set of peptides is prioritized according to one or moreof the following ordered set of criteria: unique peptides first, thennon-unique; peptides with no observed post-translational modificationsfirst, then those observed with post-translational modifications;peptides within the mass range 800-3500 Da first, then those outside of800-3500 Da; and sorted by decreasing number of variant residues. Incertain embodiments, the peptides are unique in that they only appearonce among the peptides run in a single assay.

In one embodiment, each set of peptides is prioritized according to allof the ordered set of criteria. In another embodiment, each prioritizedset of peptides contains 1-5 peptides.

In certain embodiments of the preceding methods, the two best peptidesper protein and the two best transitions per peptide are selected basedon experimental data resulting from LC-SRM-MS analysis of one or more ofthe following experimental samples: a biological disease sample, abiological control sample, and a mixture of synthetic peptides ofinterest. In a particular embodiment, the biological disease andbiological control samples are processed using an immunodepletion methodprior to LC-SRM-MS analysis. In another embodiment, the experimentalsamples contain internal standard peptides. In yet another embodiment,the LC-SRM-MS analysis method specifies a maximum of 7000 transitions,including transitions of the internal standard peptides and transitions.In other embodiments the method specifies a maximum of between1000-7000, 2000-6000, 3000-5000 and about 3500 transitions.

In one embodiment of the method, the top two transitions per peptide areselected according to one or more of the following criteria thetransitions exhibit the largest peak areas measured in either of the twobiological experimental samples; the transitions are not interfered withby other ions; the transitions do not exhibit an elution profile thatvisually differs from those of other transitions of the same peptide; orthe transitions are not beyond the detection limit of both of the twobiological experimental samples.

In another embodiment of the method, the top two peptides per proteinare selected according to one or more of the following criteria: one ormore peptides exhibit two transitions and represent the largest combinedpeak areas of the two transitions; or one or more peptides exhibit onetransition and represent the largest combined peak areas of the twotransitions.

In another aspect, provided herein is an assay developed according tothe foregoing method, and embodiments thereof.

In yet another aspect provided herein is the use of an assay developedaccording to the foregoing method, and embodiments thereof, to detect aplurality of at least 200 proteins in a single biological sample.

In another aspect, provided herein is an assay developed according tothe foregoing method, and embodiments thereof.

The disclosure provides a use of a composition, as described above, forthe development of an assay to detect a disease, disorder or conditionin a mammal.

The disclosure provides a method comprising analyzing a composition, asdescribed above, using mass spectrometry. The method can use selectedreaction monitoring mass spectrometry.

DETAILED DESCRIPTION

The present disclosure relates to methods for developing peptides andtransitions for a single sample selected reaction monitoring massspectrometry (LC-SRM-MS) assay, generally comprising the steps ofproviding a set of proteins; identifying representative proteolyticpeptides for each protein according to a set of criteria; identifyingrepresentative transitions for each peptide according to another set ofcriteria; and selecting the optimum peptides per protein and the optimumtransitions per peptide.

Selected reaction monitoring mass spectrometry is capable of highlysensitive and accurate protein quantification based on thequantification of proteolytic peptides. In terms of clinical utility,mass spectrometry-based assays are often compared to immunoassays (e.g.,Enzyme-Linked Immunosorbent Assay, or ELISA), which have the ability toquantify specific analytes in large sample sets (e.g., 96 or 384 samplesin parallel microtitre plate-based format). Until recently, massspectrometry-based protein assays were not able to match these samplesizes or quantitative accuracy. Considerable time and expense isrequired to generate and characterize antibodies required forimmunoassays. Increasingly efficient LC-SRM-MS assays, therefore, maysurpass immunoassays such as ELISA in the rapid development ofclinically useful, multiplexed protein assays.

LC-SRM-MS is a highly selective method of tandem mass spectrometry whichhas the potential to effectively filter out all molecules andcontaminants except the desired analyte(s). This is particularlybeneficial if the analysis sample is a complex mixture which maycomprise several isobaric species within a defined analytical window.LC-SRM-MS methods may utilize a triple quadrupole mass spectrometerwhich, as is known in the art, includes three quadrupole rod sets. Afirst stage of mass selection is performed in the first quadrupole rodset, and the selectively transmitted ions are fragmented in the secondquadrupole rod set. The resultant transition (product) ions are conveyedto the third quadrupole rod set, which performs a second stage of massselection. The product ions transmitted through the third quadrupole rodset are measured by a detector, which generates a signal representativeof the numbers of selectively transmitted product ions. The RF and DCpotentials applied to the first and third quadrupoles are tuned toselect (respectively) precursor and product ions that have m/z valueslying within narrow specified ranges. By specifying the appropriatetransitions (m/z values of precursor and product ions), a peptidecorresponding to a targeted protein may be measured with high degrees ofsensitivity and selectivity. Signal-to-noise ratio in LC_SRM_MS is oftensuperior to conventional tandem mass spectrometry (MS/MS) experiments,that do not selectively target (filter) particular analytes but ratheraim to survey all analytes in the sample.

Accordingly, provided herein is a method for developing peptides andtransitions for a plurality of proteins for use in selected reactionmonitoring mass spectrometry (LC-SRM-MS) assay. In a preferredembodiment, the assay involves the analysis of a single samplecontaining all analytes of interest (e.g., a proteolytic digest ofplasma proteins). As to the selection of the protease(s) used, trypsin,which cleaves exclusively C-terminal to arginine and lysine residues, isa preferred choice to generate peptides because the masses of generatedpeptides are compatible with the detection ability of most massspectrometers (up to 2000 m/z), the number and average length ofgenerated peptides, and also the availability of efficient algorithmsfor the generation of databases of theoretical trypsin-generatedpeptides. High cleavage specificity, availability, and cost are otheradvantages of trypsin. Other suitable proteases will be known to thoseof skill in the art. Miscleavage is a factor for failure or ambiguousprotein identification. A miscleavage can be defined as partialenzymatic protein cleavages generating peptides with internal missedcleavage sites reflecting the allowed number of sites (targeted aminoacids) per peptide that were not cut. The presence of post-translationalmodifications (PTMs) is also a potential contributor to the problem ofmiscleavages.

LC-SRM-MS mass spectrometry involves the fragmentation of gas phase ionsand occurs between the different stages of mass analysis. There are manymethods used to fragment the ions and these can result in differenttypes of fragmentation and thus different information about thestructure and composition of the molecule. The transition ions observedin an LC-SRM-MS spectrum result from several different factors, whichinclude, but are not limited to, the primary sequence, the amount ofinternal energy, the means of introducing the energy, and charge state.Transitions must carry at least one charge to be detected. An ion iscategorized as either a, b or c if the charge is on a transitioncomprising the original N terminus of the peptide, whereas the ion iscategorized as either x, y or z if the charge is on a transitioncomprising the original C terminus of the peptide. A subscript indicatesthe number of residues in the transition (e.g., one peptide residue inx₁, two peptide residues in y₂, and three peptide residues in z₃, etc.).

In a generic peptide repeat unit represented —N—C(O)—C—, an x ion and ana ion resulting from cleavage of the carbonyl-carbon bond (i.e.,C(O)—C). The x ion is an acylium ion, and the a ion is an iminium ion. Ay ion and a b ion result from cleavage of the carbonyl-nitrogen bond(i.e., C(O)—N, also known as the amide bond). In this case, the y ion isan ammonium ion and the b ion is an acylium ion. Finally, a z ion and ac ion result from cleavage of the nitrogen-carbon (i.e., C—N) bond. Thez ion is a carbocation and the c ion is an ammonium ion.

Superscripts are sometimes used to indicate neutral losses in additionto the backbone fragmentation, for example, * for loss of ammonia and °for loss of water. In addition to protons, c ions and y ions mayabstract an additional proton from the precursor peptide. Inelectrospray ionization, tryptic peptides may carry more than onecharge.

Internal transitions arise from double backbone cleavage. These may beformed by a combination of b-type and y-type cleavage (i.e., cleavageproducing b and y ions). Internal cleavage ions may also be formed by acombination of a-type and y-type cleavage. An internal transition with asingle side chain formed by a combination of a-type and y-type cleavageis called an iminium ion (sometimes also referred to as an imonium orimmonium ion). These ions are labeled with the one letter code for thecorresponding amino acid.

Low energy CID (i.e., collision induced dissociation in a triplequadrupole or an ion trap) involves the fragmentation of a peptidecarrying a positive charge, primarily along its backbone, to generateprimarily a, b and y ions.

In one aspect, provided herein is a method for developing peptides andtransitions for a plurality of proteins for a single sample selectedreaction monitoring mass spectrometry (LC-SRM-MS) assay: (a) providing apanel or plurality of proteins; (b) identifying a set of peptides foreach protein, wherein (i) each peptide in the set of peptidescorresponds to a transition of said protein; (ii) the peptides have amonoisotopic mass of 700-5000 Da; and (iii) the peptides do not containcysteine or does not contain cysteine or methionine. In otherembodiments, each selected peptide contains cysteine or methionine. ;and; (c) identifying a set of transitions for each peptide, wherein (i)the transitions for each peptide have one of the four most intense b ory transition ions; (ii) the transitions for each peptide have m/z valuesof at least 30 m/z above or below those of the precursor ion; (iii) thetransitions for each peptide do not interfere with transitions fromother peptides; and (iv) the transitions represent transitions due tobreakage of peptide bond at different sites of the protein; and (d)selecting the peptides for each protein that best fit the criteria ofstep (b) and the transitions per peptide that best fit the criteria ofstep (c); thereby developing peptides and transitions for a LC-SRM-MSassay.

By plurality of proteins it is meant that at least 2, 3, 4, 5, 6, 7, 8,9, 10, 15, 20, 25, 50, 100, 150, 200, 250, 300, 400, 450, 500 or moreproteins. In certain embodiments, the plurality of proteins canencompass between 2 and 10, 10 and 20, 20 and 50, 50 and 100, 100 and200 or 200 and 500 proteins. In other embodiments, the plurality ofproteins can encompass between 250 and 450; or 300 and 400 proteins.

Trypsin-like proteases cleave peptide bonds following a positivelycharged amino acid (e.g., lysine (K) or arginine (R)). This specificityis driven by the residue which lies at the base of the enzyme's S1pocket (generally a negatively charged aspartic acid or glutamic acid).Accordingly, in one embodiment of the method, the peptides do notinclude any peptide that is bounded by KK, KR, RK or RR, either upstreamof downstream in the corresponding protein sequence. In anotherembodiment, each peptide of said set of peptides is unique to thecorresponding protein.

Post-translational modification (PTM) is the chemical modification of aprotein after its translation. It can include any modification followingtranslation, including cleavage. It is one of the later steps in proteinbiosynthesis, and thus gene expression, for many proteins. It isdesirable to avoid such peptides for the purpose of proteinidentification. Thus, in another embodiment, the peptides do not includepeptides which were observed in post-translational modified forms.

In still another embodiment, each set of peptides is prioritizedaccording to one or more of the following ordered set of criteria: (a)unique peptides first, then non-unique; (b) peptides with no observedpost-translational modifications first, then those observed withpost-translational modifications; (c) peptides within the mass range800-3500 Da first, then those outside of 800-3500 Da; and (d) sorted bydecreasing number of variant residues. In one embodiment, each set ofpeptides is prioritized according to all of the ordered set of criteria.In another embodiment, each prioritized set of peptides contains 1-5peptides.

In certain embodiments, one or more liquid chromatography (LC)purification steps are performed prior to a subsequent LC-SRM-MSanalysis step. Traditional LC analysis relies on the chemicalinteractions between sample components and column packing materials,where laminar flow of the sample through the column is the basis forseparation of the analyte of interest from the test sample. The skilledartisan will understand that separation in such columns is a diffusionalprocess. A variety of column packing materials are available forchromatographic separation of samples, and selection of an appropriateseparation protocol is an empirical process that depends on the samplecharacteristics, the analyte of interest, the interfering substancespresent and their characteristics, etc. Various packing chemistries canbe used depending on the needs (e.g., structure, polarity, andsolubility of compounds being purified). In various embodiments thecolumns are polar, ion exchange (both cation and anion), hydrophobicinteraction, phenyl, C-2, C-8, C-18 columns, polar coating on porouspolymer, or others that are commercially available. Duringchromatography, the separation of materials is effected by variablessuch as choice of eluant (also known as a “mobile phase”), choice ofgradient elution and the gradient conditions, temperature, etc. Incertain embodiments, an analyte may be purified by applying a sample toa column under conditions where the analyte of interest is reversiblyretained by the column packing material, while one or more othermaterials are not retained. In these embodiments, a first mobile phasecondition can be employed where the analyte of interest is retained bythe column, and a second mobile phase condition can subsequently beemployed to remove retained material from the column, once thenon-retained materials are washed through. Alternatively, an analyte maybe purified by applying a sample to a column under mobile phaseconditions where the analyte of interest elutes at a differential ratein comparison to one or more other materials. As discussed above, suchprocedures may enrich the amount of one or more analytes of interestrelative to one or more other components of the sample.

The following parameters are used to specify an LC-SRM-MS assay of aprotein under a particular LC-SRM-MS system: (1) a tryptic peptide ofthe protein; (2) the retention time (RT) of the peptide; (3) the m/zvalue of the peptide precursor ion; (4) the declustering potential usedto ionize the precursor ion; (5) m/z value of a fragment ion generatedfrom the peptide precursor ion; and (6) the collision energy (CE) usedto fragment the peptide precursor ion that is optimized for theparticular peptide.

In certain embodiments of the preceding methods, the two best peptidesper protein and the two best transitions per peptide are selected basedon experimental data resulting from LC-SRM-MS analysis of one or more ofthe following experimental samples: a biological disease sample, abiological control sample, and a mixture of synthetic peptides ofinterest. Biological samples include body fluids, tissue samples andcell samples. Body fluid samples can include blood, serum, sputum,genital secretions, cerebrospinal fluid, sweat or excreta such as urine.Body tissue samples can include lung, skin, brain, spine, bone, muscle,epithelial, liver, kidney, pancreas, gastrointestinal tract,cardiovascular tissue, heart or nervous tissue. Biological diseasesamples can include cancer, benign tumors, infected tissue and tissuesubject to trauma. In a particular embodiment, the biological diseaseand biological control samples are processed using an immunodepletionmethod prior to LC-SRM-MS analysis. Immunodepletion involves removal ofone or more proteins through the use of antibodies. Numerousimmunodepletion techniques are known to those of skill in the art. Inanother embodiment, the biological disease and biological controlsamples are processed using an immunocapture method prior to LC-SRM-MSanalysis. Immunocapture involves selection of one or more proteinsthrough the use of antibodies. Numerous immunocapture techniques areknown to those of skill in the art.

To facilitate accurate quantification of the peptide transitions by themethods disclosed herein, a set of isotopically-labeled syntheticversions of the peptides of interest may be added in known amounts tothe sample for use as internal standards. Since the isotopically-labeledpeptides have physical and chemical properties identical to thecorresponding surrogate peptide, they co-elute from the chromatographiccolumn and are easily identifiable on the resultant mass spectrum. Theaddition of the labeled standards may occur before or after proteolyticdigestion. Methods of synthesizing isotopically-labeled peptides will beknown to those of skill in the art. Thus, in another embodiment, theexperimental samples contain internal standard peptides. Otherembodiments may utilize external standards or other expedients forpeptide quantification.

In yet another embodiment, the LC-SRM-MS analysis method specifies amaximum of 7000 transitions, including transitions of the internalstandard peptides and transitions. As used herein, the term “transition”refers to the specific pair of m/z (mass-to-charge) values associatedwith the precursor and transition ions corresponding to a specificpeptide and, therefore, to a specific protein.

In one embodiment of the method, the top two transitions per peptide areselected according to one or more of the following criteria (A): (1) thetransitions exhibit the largest peak areas measured in either of the twobiological experimental samples; (2) the transitions are not interferedwith by other ions; (3) the transitions do not exhibit an elutionprofile that visually differs from those of other transitions of thesame peptide; (4) the transitions are not beyond the detection limit ofboth of the two biological experimental samples; (5) the transitions donot exhibit interferences.

For the mass spectrometric analysis of a particular peptide, thequantities of the peptide transitions in the sample may be determined byintegration of the relevant mass spectral peak areas, as known in theprior art. When isotopically-labeled internal standards are used, asdescribed above, the quantities of the peptide transitions of interestare established via an empirically-derived or predicted relationshipbetween peptide transition quantity (which may be expressed asconcentration) and the area ratio of the peptide transition and internalstandard peaks at specified transitions.

In another embodiment of the method, the top two peptides per proteinare selected according to one or more of the following criteria (B): (1)one or more peptides exhibit two transitions according to criteria (A)and represent the largest combined peak areas of the two transitionsaccording to criteria (A); and (2) one or more peptides exhibit onetransition according to criteria (A) and represent the largest combinedpeak areas of the two transitions according to criteria (A).

Assays

The methods of the present disclosure allow the quantification of highabundance and low abundance plasma proteins that serve as detectablemarkers for various health states (including diseases and disorders),thus forming the basis for assays that can be used to determine thedifferences between normal levels of detectable markers and changes ofsuch detectable markers that are indicative of changes in health status.In one aspect of the disclosure, provided herein is an assay developedaccording to the foregoing method, and embodiments thereof. In anotheraspect, provided herein is the use of an assay developed according tothe foregoing method, and embodiments thereof, to detect a plurality ofat least 200, 300 or more proteins in a single sample.

Definitions

As used herein, “transition” refers to a pair of m/z values associatedwith a peptide. Normally, labeled synthetic peptides are used as qualitycontrols in SRM assays. However, for very large SRM assays, labeledpeptides are not feasible. However, correlation techniques (Keary,Butler et al. 2008) were used to confirm the identity of proteintransitions with high confidence. The correlation between a pair oftransitions is obtained from their expression profile over all samplesin the training set study detailed below. As expected, transitions fromthe same peptide are highly correlated. Similarly, transitions fromdifferent peptide fragments of the same protein are also highlycorrelated. In contrast, transitions form different proteins are nothighly correlated. This methodology enables a statistical analysis ofthe quality of the protein's SRM assay. For example, if the correlationof the transitions from the two peptides from the same protein is above0.5 then there is less than a 5% probability that the assay is false

As used herein, a “tryptic peptide” refers to the peptide that is formedby the treatment of a protein with trypsin.

As used herein, “RT” refers to “retention time”, the elapsed timebetween injection and elution of an analyte.

As used herein, “m/z” indicates the mass-to-charge ratio of an ion.

As used herein “DP” refers to the “declustering potential”, a voltagepotential to dissolvate and dissociate ion clusters. It is also known as“fragmentor voltage” or “ion transfer capillary offset voltage”depending upon the manufacturer.

As used herein, “CE” refers to “collision energy”, the amount of energyprecursor ions receive as they are accelerated into the collision cell.

As used herein, “LC-SRM-MS” is an acronym for “selected reactionmonitoring” and may be used interchangeably with “LC-MRM-MS”.

As used herein, “MS/MS” represents tandem mass spectrometry, which is atype of mass spectrometry involving multiple stages of mass analysiswith some form of fragmentation occurring in between the stages.

As used herein, “ISP” refers to “internal standard peptides”.

As used herein, “HGS” refers to “human gold standard”, which iscomprised of a pool of plasma from healthy individuals.

As used herein, “MGF” refers to “Mascot generic file”. Mascot is asearch engine that uses mass spectrometry data to identify proteins fromprimary sequence databases. A Mascot generic file is a plain text(ASCII) file containing peak list information and, optionally, searchparameters.

Mascot is a tool for assessing mass spectrometry data against proteinsequences. This data can be acquired from any mass spectrometrytechnique including MALDI-TOF and electrospray ionization MS (includingLC-SRM-MS) data. Mascot uses a ‘probability-based MOWSE’ algorithm toestimate the significance of a match (i.e., that the observedtransitions correspond to a particular protein). The total score is theabsolute probability that the observed match is a random event. They arereported as −10×LOG10(P), where P is the absolute probability. Lowerprobabilities, therefore, are reported as higher scores. For example, ifthe absolute probability that an observed match is random is 1×10⁻¹²,Mascot reports it as 120.

The disclosure also provides compositions. These compositions caninclude any of the transition ions described in Table II. Thesetransition ions exist while peptides derived from the proteins in TableII are undergoing analysis with LC-SRM-MS. In one embodiment, thecomposition includes any of the transition ions described in Table II.In another embodiment, the composition includes any two transition ionsdescribed in Table II. In other embodiments, the composition includes,any 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25,30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120,130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260,270, 280, 290, 300 or 331 transition ions described in Table II.

In another embodiment, each of the transition ions in the compositioncorresponds and/or is derived from a different protein. In anotherembodiment, 90% of the transition ions in the composition correspondwith and/or are derived from a protein that no other transition ion inthe composition corresponds. In other embodiments, 80, 70, 60, 50, 40,30, 20, 10 or 0% of the transition ions in the composition correspondand/or are derived from a protein that no other transition ion in thecomposition corresponds.

The compositions described herein included synthetic peptides. Syntheticpeptides can be used as controls for the abundance of proteins they arederived from and/or correspond. In certain embodiments, the abundance ofthe synthetic peptides is defined and the results are compared toLC-SRM-MS results from a peptide found in a sample to the LC-SRM-MSresults in the corresponding synthetic peptide. This allows for thecalculation of the abundance of the peptide in the sample. In certainembodiments, by knowing the abundance of a peptide in a sample, theabundance of the protein it corresponded to is determined.

Synthetic peptides can be generated using any method known in the art.These methods can include recombinant expression techniques such asexpression in bacteria or in vitro expression in eukaryotic cell lysate.These methods can also include solid phase synthesis.

In one embodiment, the composition includes synthetic peptides selectedfrom any of the peptides described in Table II. In another embodiment,the composition included any two peptides described in Table II. Inother embodiments, the composition included, any 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55,60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170,180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 331 ormore peptides described in Table II.

In another embodiment, each of the peptides in the composition eachcorresponds with a different protein. In another embodiment, 90% of thepeptides in the composition correspond with a protein that no otherpeptide in the composition corresponds with. In other embodiments, 80,70, 60, 50, 40, 30, 20, 10 or 0% of the peptides in the compositioncorrespond with from a protein that no other peptide in the compositioncorresponds with.

The peptides can be isotopically labeled. The isotopes with which theycan be labeled include ¹³C, ²H, ¹⁵N and ¹⁸O. The peptides can alsoinclude a polar solvent. Polar solvents can include water and mixturesof ethanol and water.

In certain embodiments, the samples described herein are taken frommammals. These mammals include rats, mice, rabbits, dogs, non-humanprimates and humans. Samples can be isolated from any tissue or organ orfrom any bodily fluid. Organs from which samples can be taken includeskin, heart, lung, brain, kidney, liver, pancreas, spleen, testes,ovaries, gall bladder, thymus, thyroid, eye, ear, nose, mouth, tongue,penis, vagina, bladder or larynx. Tissues include nervous tissue,vascular tissue, muscle, bone, gastrointestinal tract, epithelialtissue, fibroblastic tissue, mucous membranes, hair, skin, reproductivetissue and connective tissue. Body fluids and excretions include, blood,serum, saliva, urine, semen, vaginal secretions, excrement, bile, tears,lymph, ear wax, mucous, shed skin, finger nails, toe nails, skin oils,sweat and dandruff.

The relative abundance of one or more of the proteins represented by thetransition ions and synthetic peptides described above can be used todiagnose, determine likelihood of the presence of, develop prognoses forand/or stage various diseases and pathologies. Often the organ, tissueor bodily fluid or excretion from which the sample is taken is distinctfrom the organ, tissue or bodily fluid or excretion involved with thedisease or pathology. For example, the presence of Alzheimer's diseasecan be determined from a sample taken from blood. Any type of body fluidmay be used in the assays.

Diseases and pathologies that status, diagnosis, presence or prognosiscan be found using the transition ions and/or synthetic peptidesdescribed herein include cancer, metabolic diseases, neurologicaldisorders, infectious diseases and cardiovascular disorders.

EXAMPLES I. Exemplary Standard Operating Procedure Protein Selection

Proteins known to be over-expressed or under-expressed in Alzheimer'sdisease patients were obtained (through literature searching,experimental data or proprietary databases) as shown in Table I. The setof proteins was reduced to a set of 357 proteins (see Table II) byprioritizing those proteins that have been previously detected myLC-MS/MS in blood (serum or plasma).

Selected proteins were then identified by their UniProt protein name andaccession, their Entrez gene symbol and gene name, the isoform accessionand their amino acid sequence. The canonical isoform in UniProt wasselected if a protein has more than one isoform.

Peptide Selection for Synthesis

The five best peptides per protein for LC-SRM-MS assay were selected foras follows. Fully tryptic peptides having a monoisotopic mass of800-3500 mass units, without miscleavages, not containing a cysteine (C)or a methionine (M), without having high miscleavage probability wereselected. Further, any peptide that was bounded by KK, KR, RK or RR(either upstream or downstream) in the corresponding protein sequencewas not selected.

Peptides were selected that were unique to the protein of interest.Peptides were only selected that match only one protein or proteinfamily including analogues of the one protein, when searched in proteindatabases. Further, peptides which were observed in post-translationalmodified forms were not selected. Databases were assessed that showedexpression of the proteins from which the peptides were isolated inhuman blood. Also databases of good quality MS peptides were searched.Peptides that appeared in human blood and were good quality MS peptideswere favored. If these methods did not result in a sufficient number ofpeptides, rules were relaxed in a step wise manner to allow a greaternumber of peptides until a sufficient number was reached. The purity ofthe synthesized peptides was >75% and the amount of material was ≧25 μg.Peptides did not need to be desalted.

The four best transitions per peptide are then selected and optimizedbased on experimental results from a mixture of synthetic peptides.LC-SRM-MS-triggered MS/MS spectra was acquired for each syntheticpeptide, using a QTRAP 5500 instrument. One spectrum or the doubly—andone for the triply—charged precursor ion was collected for each of theidentified peptides (Mascot score ≧15), retention time was recorded forthe four most intense b or y transition ions. The selected transitionions possessed m/z values were at least 30 m/z above or below those ofthe precursor ions; they did not interfere with other syntheticpeptides; and they were transition ions due to breakage of peptide bondat different sites.

If an insufficient percentage of the synthetic peptides were acquired,the steps were repeated. In some cases, the second transition with firstwith theoretical y+ ions with m/z values at least 30 m/z above those ofthe doubly charged precursor ion was selected if an insufficientpercentage was acquired. Peptides that failed to trigger the acquisitionof MS/MS spectrum were discarded.

II. Exemplary Protein list

The abundance of the following proteins can be assessed substantiallysimultaneously using the MS-LC-SRM-MS system described herein.Transitions from these proteins can be used to diagnose diseasesincluding Alzheimer's disease when their abundance is measured in abiological specimen from a subject to be diagnosed for Alzheimer'sdisease. In one embodiment, the abundances of these proteins are measurein the blood serum of the subject.

Lengthy table referenced here US20150168421A1-20150618-T00001 Pleaserefer to the end of the specification for access instructions.

Lengthy table referenced here US20150168421A1-20150618-T00002 Pleaserefer to the end of the specification for access instructions.

VI. Exemplary Assayed Protein

The expression of the following 357 proteins were assessed substantiallysimultaneously using the MS-LC-SRM-MS system described herein.

41_HUMAN

5HT2C_HUMAN

A1AG1_HUMAN

A1AG2_HUMAN

A1BG_HUMAN

A2MG_HUMAN

A4_HUMAN

AACT_HUMAN

ABCA1_HUMAN

ACBD7_HUMAN

ACE2_HUMAN

ACHA2_HUMAN

ACHA4_HUMAN

ACHAS_HUMAN

ACHB_HUMAN

ACHB2_HUMAN

ADA12_HUMAN

ADA23_HUMAN

AFAM_HUMAN

AGAL_HUMAN

AGAP2_HUMAN

ALBU_HUMAN

ALS_HUMAN

AMFR2_HUMAN

AMNLS_HUMAN

AMPB_HUMAN

ANGP1_HUMAN

ANGT_HUMAN

ANO3_HUMAN

ANT3_HUMAN

AP1B1_HUMAN

APC2_HUMAN

APLP1_HUMAN

APOA1_HUMAN

AP0A2_HUMAN

AP0A4_HUMAN

APOB_HUMAN

APOC2_HUMAN

APOD_HUMAN

APOE_HUMAN

APOL4_HUMAN

APOOL_HUMAN

ARHG7_HUMAN

ARP21_HUMAN

ARSA_HUMAN

ARSE_HUMAN

ARTN_HUMAN

ASGR1_HUMAN

AT12A_HUMAN

AT2A2_HUMAN

AT2B3_HUMAN

ATS1_HUMAN

BAX_HUMAN

BCAS1_HUMAN

BDNF_HUMAN

BEST1_HUMAN

BTNL8_HUMAN

C1QL2_HUMAN

C1QT4_HUMAN

CACB2_HUMAN

CAD11_HUMAN

CAD19_HUMAN

CAD22_HUMAN

CADH3_HUMAN

CADH5_HUMAN

CADH7_HUMAN

CALL3_HUMAN

CAMKV_HUMAN

CAR14_HUMAN

CATD_HUMAN

CB080_HUMAN

CB085_HUMAN

CBPN_HUMAN

CD3D_HUMAN

CD72_HUMAN

CEL3A_HUMAN

CEL3B_HUMAN

CERU_HUMAN

CETP_HUMAN

CF072_HUMAN

CFAB_HUMAN

CFAH_HUMAN

CHAD_HUMAN

CK041_HUMAN

CLC4M_HUMAN

CLUS_HUMAN

CNTN1_HUMAN

CNTN2_HUMAN

CO1A2_HUMAN

CO2_HUMAN

CO3_HUMAN

CO4A_HUMAN

CO4A4_HUMAN

CO4B_HUMAN

C06_HUMAN

CO8A_HUMAN

CO9A2_HUMAN

COIA1_HUMAN

CORT_HUMAN

CP46A_HUMAN

CPLX2_HUMAN

CRLF1_HUMAN

CRUM1_HUMAN

CSF1_HUMAN

CSF1R_HUMAN

DBC1_HUMAN

DCBD1_HUMAN

DCBD2_HUMAN

DDR2_HUMAN

DIRA2_HUMAN

E41L3_HUMAN

EAA2_HUMAN

EDNRB_HUMAN

ELAV3_HUMAN

EMIL2_HUMAN

EMIL3_HUMAN

EPHA8_HUMAN

ERLN1_HUMAN

ERMIN_HUMAN

ERO1B_HUMAN

F123A_HUMAN

F13A_HUMAN

FA20A_HUMAN

FCGRN_HUMAN

FETUA_HUMAN

FEZ1_HUMAN

FGFR2_HUMAN

FGFR3_HUMAN

FGL1_HUMAN

FIBA_HUMAN

FIBB _HUMAN

FIBG_HUMAN

FINC_HUMAN

FRS2_HUMAN

GABR2_HUMAN

GALR3_HUMAN

GAS6_HUMAN

GBRA2_HUMAN

GBRB2_HUMAN

GELS_HUMAN

GFRA2_HUMAN

GNAQ_HUMAN

GOLM1_HUMAN

GOPC_HUMAN

GP113_HUMAN

GP125_HUMAN

GP158_HUMAN

GP2_HUMAN

GPC5_HUMAN

GPC5D_HUMAN

GPC6_HUMAN

GPR88_HUMAN

GRIA2_HUMAN

GRM5_HUMAN

GRN_HUMAN

GT253_HUMAN

HAS1_HUMAN

HCN1_HUMAN

HCN2_HUMAN

HEMO_HUMAN

HEP2_HUMAN

HPCA_HUMAN

HPT_HUMAN

HRG_HUMAN

HS3S5_HUMAN

I12R1_HUMAN

IC1_HUMAN

ICAM3_HUMAN

IGF1R_HUMAN

IL12B _HUMAN

IL1AP_HUMAN

IL1R2_HUMAN

INADL_HUMAN

INHBA_HUMAN

IPSP_HUMAN

ITA3_HUMAN

ITAM_HUMAN

ITB2_HUMAN

ITB5_HUMAN

ITIH1_HUMAN

ITIH2_HUMAN

ITIH3_HUMAN

ITIH4_HUMAN

JPH3_HUMAN

KAIN_HUMAN

KALRN_HUMAN

KCC1G_HUMAN

KCC2A_HUMAN

KCNA1_HUMAN

KCNA2_HUMAN

KCNA3_HUMAN

KCNA5_HUMAN

KCNQ1_HUMAN

KCNV2_HUMAN

KCTD4_HUMAN

KIF5A_HUMAN

KIRR2_HUMAN

KLK3_HUMAN

KLKB1_HUMAN

KNG1_HUMAN

KSYK_HUMAN

LAMB2_HUMAN

LAT2_HUMAN

LAT3_HUMAN

LCK_HUMAN

LCN8_HUMAN

LGI1_HUMAN

LGMN_HUMAN

LIPE_HUMAN

LRMP_HUMAN

LRP8_HUMAN

LRTM2_HUMAN

LSHR_HUMAN

LTBP1_HUMAN

LYG2_HUMAN

MAMC2_HUMAN

MAP4_HUMAN

MICA_HUMAN

MMP1_HUMAN

MMP16_HUMAN

MMP17_HUMAN

MMP2_OHUMAN

MMP24_HUMAN

MMP9_HUMAN

MOT2_HUMAN

MPDZ_HUMAN

MTOR_HUMAN

MYP2_HUMAN

NCAN_HUMAN

NCIOC2_HUMAN

NDF6_HUMAN

NECP2_HUMAN

NETO1_HUMAN

NETR_HUMAN

NEUG_HUMAN

NEUM_HUMAN

NFL_HUMAN

NKX62_HUMAN

NMDE1_HUMAN

NMDE3_HUMAN

NMDZ1_HUMAN

NMS_HUMAN

NOE3_HUMAN

NPT4_HUMAN

NPTX1_HUMAN

NRG3_HUMAN

NTRK2_HUMAN

ODP2_HUMAN

OLFL3_HUMAN

OLIG1_HUMAN

OPCM_HUMAN

OTOAN_HUMAN

P2RX1_HUMAN

P4K2A_HUMAN

PACN1_HUMAN

PAK3_HUMAN

PAQR6_HUMAN

PAR6B_HUMAN

PARD3_HUMAN

PARK7_HUMAN

PCD1S_HUMAN

PCDA5_HUMAN

PCDAA_HUMAN

PCDB6_HUMAN

PCDB7_HUMAN

PCDBC_HUMAN

PCDBF_HUMAN

PCDGE_HUMAN

PCDGF_HUMAN

PCSK1_HUMAN

PDIA2_HUMAN

PDYN_HUMAN

PEDF_HUMAN

PERL_HUMAN

PGCB_HUMAN

PGCP_HUMAN

PICAL_HUMAN

PIN1_HUMAN

PKDRE_HUMAN

PLCB1_HUMAN

PON1_HUMAN

PRIO_HUMAN

PSMG1_HUMAN

PTN5_HUMAN

PTPRB_HUMAN

PTPRO_HUMAN

PTPRT_HUMAN

PVRL1_HUMAN

PZP_HUMAN

RCN1_HUMAN

RELN_HUMAN

RES18_HUMAN

RGS11_HUMAN

RGS2O_HUMAN

RGS4_HUMAN

RRAGC_HUMAN

RUN3A_HUMAN

S12A5_HUMAN

S12A6_HUMAN

S15A2_HUMAN

S39A4_HUMAN

SAA4_HUMAN

SCG1_HUMAN

SCG3_HUMAN

SCN2A_HUMAN

SCNNA_HUMAN

SCRT1_HUMAN

SEM4A_HUMAN

SEMG1_HUMAN

SEPP1_HUMAN

SEPT3_HUMAN

SGCZ_HUMAN

SHSA7_HUMAN

SIA8C_HUMAN

SIG12_HUMAN

SIX3_HUMAN

SLIK1_HUMAN

SLIT1_HUMAN

SNP25_HUMAN

SNTB1_HUMAN

SO1A2_HUMAN

SO1B3_HUMAN

SPB5_HUMAN

SREC_HUMAN

STH_HUMAN

SYN2_HUMAN

SYNPR_HUMAN

SYTL4_HUMAN

SYUA_HUMAN

SYUB_HUMAN

T151A_HUMAN

TADBP_HUMAN

TAU_HUMAN

TBB2B_HUMAN

TERA_HUMAN

TFR2_HUMAN

TLR7_HUMAN

TM9S1_HUMAN

TMPS2_HUMAN

TNF6B _HUMAN

TNR19_HUMAN

TR11B _HUMAN

TRFR_HUMAN

TRIM9_HUMAN

TRPV5_HUMAN

TYRO_HUMAN

UGGG2_HUMAN

UNC5C_HUMAN

VGFR3_HUMAN

VTDB_HUMAN

VTNC_HUMAN

WNK4_HUMAN

WNT8B _HUMAN

XLRS1_HUMAN

YQ051_HUMAN

ZIC1_HUMAN

ZIC2_HUMAN

LENGTHY TABLES The patent application contains a lengthy table section.A copy of the table is available in electronic form from the USPTO website(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20150168421A1).An electronic copy of the table will also be available from the USPTOupon request and payment of the fee set forth in 37 CFR 1.19(b)(3).

1. A multiplexed LC-SRM-MS assay for the measurement of a plurality ofproteins in a single sample comprising: a) generating a set of optimalpeptides and corresponding transitions for each protein monitored; b)optimizing the collision energy for each transition such thatinterference among the transitions monitored is avoided; c) selecting aset of transitions that have the greatest peak areas are monitored foreach of the proteins, and wherein the selected transitions do notinterfere with the ions in the sample; d) monitoring the detected set oftransitions for each protein in the sample, there-by measuring aplurality of proteins in the sample.
 2. The assay of claim 1, whereineach monitored peptide (i) has a monoisotopic mass of 700-5000 Da; and(ii) does not contain a cysteine or a methionine; and.
 3. The assay ofclaim 1, wherein the transitions for each peptide (i) have one of thefour most intense b or y transition ions; (ii) has m/z values of atleast 30 m/z above or below those of a precursor ion; (iii) do notinterfere with transitions from other peptides; and (iv) representtransitions due to breakage of peptide bond at different sites of theprotein.
 4. The assay according to claim 1, wherein the peptides do notinclude any peptide that is bounded by KK, KR, RK or RR, either upstreamof downstream in the corresponding protein sequence.
 5. The assayaccording to claim 1, wherein each peptide of said set of peptides isunique to the corresponding protein.
 6. The assay according to claim 1,wherein the peptides do not include peptides which were observed inpost-translational modified forms.
 7. The assay according to claim 1,wherein each set of peptides is prioritized according to one or more ofthe following ordered set of criteria: (a) unique peptides first, thennon-unique; (b) peptides with no observed post-translationalmodifications first, then those observed with post-translationalmodifications; (c) peptides within the mass range 800-3500 Da first,then those outside of 800-3500 Da; and (d) sorted by decreasing numberof variant residues.
 8. The assay according to claim 7, wherein each setof peptides is prioritized according to all of the ordered set ofcriteria.
 9. The assay according to any one of claim 7 or 8, whereineach prioritized set of peptides contains 1-5 peptides.
 10. The assayaccording to any one of claims 1-9, wherein the two best peptides perprotein and the two best transitions per peptide are selected based onexperimental data resulting from LC-SRM-MS analysis of one or more ofthe following experimental samples: a biological disease sample, abiological control sample, and a mixture of synthetic peptides ofinterest.
 11. The assay according to claim 10, wherein the biologicaldisease and biological control samples are processed using animmunodepletion method prior to LC-SRM-MS analysis.
 12. The assayaccording to claim 11, wherein the experimental samples contain internalstandard peptides.
 13. The assay according to claim 11, wherein theLC-SRM-MS analysis method specifies a maximum of 7000 transitions,including transitions of the internal standard peptides and transitions.14. The assay according to claim 1, wherein the top two transitions perpeptide are selected according to one or more of the following criteria:(1) the transitions exhibit the largest peak areas measured in either ofthe two biological experimental samples; (2) the transitions are notinterfered with by other ions; (3) the transitions do not exhibit anelution profile that visually differs from those of other transitions ofthe same peptide; (4) the transitions are not beyond the detection limitof both of the two biological experimental samples; and (5) thetransitions do not exhibit interferences.
 15. The assay according toclaim 1, wherein the top two peptides per protein are selected accordingto one or more of the following criteria: (1) one or more peptidesexhibit two transitions according to claim 12 and represent the largestcombined peak areas of the two transitions according to claims 12; and(2) one or more peptides exhibit one transition according to claim 12and represent the largest combined peak areas of the two transitionsaccording to claim
 12. 16. An assay developed according to the method ofclaim 1.